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The sqlite3.dll that ships with calibre is the one that comes with python 2.7.8. I am not going to replace it, because replacing DLLs willy nilly is a recipe for disaster. Nor should you. Especially on windows where C runtime libraries are all mutually incompatible and depend on compiler version.
There's nothing preventing you from using calibre's DB API across multiple libraries, that's how the calibre copy to library function works.
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